Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Metabolite annotation and identification

MS-FINDER

Explore formula and structure candidates using fragmentation rules and EI-MS or MS/MS library searches.

LC-MSGC-MSDesktop graphical interfaceCommand lineSource available with restrictions
Access toolSuggest an update

Overview

MS-FINDER combines formula prediction, fragment interpretation and structure ranking. Its graphical and console interfaces support spectral-library searching and in silico prediction. It operates on prepared spectra, making it a companion to upstream processing tools.

Also known as: MSFINDER

What can this tool do?

Molecular-formula predictionStructure elucidationSpectral-library matching

Common uses

  • Rank candidate formulas and structures for unknown spectra.
  • Search EI-MS or MS/MS libraries through the GUI or a batch console job.

Scientific fit

Primary function

Metabolite annotation and identification

Data compatibility

Inputs

Mass spectra, Spectral library

Outputs

Compound list or annotations, Human-readable report

Input formats

MSP, MS-FINDER MAT (spectral text format)

Output formats

MS-FINDER ASCII result files

Scope and considerations

Designed for

  • Interpretation of prepared small-molecule mass spectra.

Not designed for

  • Replacing raw-data peak detection and alignment.

Important requirements

  • Prepare MSP or MS-FINDER MAT files and configure precursor and mass-error settings. Check distribution requirements before installation.

Considerations

  • Fragmentation rules and library coverage constrain the result; review ambiguous candidates and retain the parameter file.

Education

Learn this tool

External tutorials and workshops collected by Navigator. Entries marked Needs review have not been checked end to end.

MS-DIAL 5 to MS-FINDER for unknown annotationMS-DIAL project · Video · Needs reviewMS-FINDER tutorialMS-FINDER project · Tutorial

Browse all education resources →

Access and documentation

Primary accessDocumentation

Software and source are publicly accessible. Check the license for the chosen distribution and the separate terms of bundled spectral libraries.

Evidence and review

Editorial review on 7 September 2026 against official documentation and the sources listed here. Scope and practical guidance are editorial synthesis; software execution and service availability were not validated.

Core publications

Resource papers, direct updates and tool-specific methods. Selection policy.

  1. Tsugawa H, Kind T, Nakabayashi R, et al. Hydrogen Rearrangement Rules: Computational MS/MS Fragmentation and Structure Elucidation Using MS-FINDER Software. Anal Chem 88, 7946-7958 (2016). doi:10.1021/acs.analchem.6b00770

Related tools

MetFragAlternative to · Rank candidate molecular structures by comparing predicted fragments with an experimental MS/MS spectrum.MS-DIALComplementary to · A graphical and command-line workbench for untargeted metabolomics and lipidomics data processing across multiple chromatography and mass spectrometry platforms.MassBankUses · Find and download open reference mass spectra with compound and acquisition metadata.

Entry history

Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.

  1. 2026-09-08 · Entry update

    Audit core publications across existing tools

    View change · Entry at this revision
  2. 2026-09-07 · First committed entry

    Expand and document 31 metabolomics tools and resources

    View change · Entry at this revision

Full GitHub history